Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.25 kDa 
• Atom Count: 1646 
• Modelled Residue Count: 195 
• Deposited Residue Count: 210 
• Unique protein chains: 1

5IN7

X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN

• PDB DOI: 10.2210/pdb5IN7/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-03-07 Released: 2016-03-23 
• Deposition Author(s): Ruf, A., Benz, J., Burger, D., D'Arcy, B., Debulpaep, M., Di Lello, P., Fry, D., Huber, W., Kremer, T., Laeremans, T., Matile, H., Ross, A., Rudolph, M.G., Rufer, A.C., Sharma, A., Steinmetz, M.O., Steyaert, J., Schoch, G., Stihle, M., Thoma, R.
• Funding Organization(s): European Molecular Biology Organization, Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.236 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

Literature

Crystal Structures of the Human Doublecortin C- and N-terminal Domains in Complex with Specific Antibodies.

Burger, D., Stihle, M., Sharma, A., Di Lello, P., Benz, J., D'Arcy, B., Debulpaep, M., Fry, D., Huber, W., Kremer, T., Laeremans, T., Matile, H., Ross, A., Rufer, A.C., Schoch, G., Steinmetz, M.O., Steyaert, J., Rudolph, M.G., Thoma, R., Ruf, A.

(2016) J Biol Chem 291: 16292-16306

• PubMed: 27226599 
• DOI: 10.1074/jbc.M116.726547
• Primary Citation of Related Structures:  
  5IKC, 5IN7, 5IO9, 5IOI, 5IP4


• PubMed Abstract: 
  

Doublecortin is a microtubule-associated protein produced during neurogenesis. The protein stabilizes microtubules and stimulates their polymerization, which allows migration of immature neurons to their designated location in the brain. Mutations in the gene that impair doublecortin function and cause severe brain formation disorders are located on a tandem repeat of two doublecortin domains. The molecular mechanism of action of doublecortin is only incompletely understood. Anti-doublecortin antibodies, such as the rabbit polyclonal Abcam 18732, are widely used as neurogenesis markers. Here, we report the generation and characterization of antibodies that bind to single doublecortin domains. The antibodies were used as tools to obtain structures of both domains. Four independent crystal structures of the N-terminal domain reveal several distinct open and closed conformations of the peptide linking N- and C-terminal domains, which can be related to doublecortin function. An NMR assignment and a crystal structure in complex with a camelid antibody fragment show that the doublecortin C-terminal domain adopts the same well defined ubiquitin-like fold as the N-terminal domain, despite its reported aggregation and molten globule-like properties. The antibodies' unique domain specificity also renders them ideal research tools to better understand the role of individual domains in doublecortin function. A single chain camelid antibody fragment specific for the C-terminal doublecortin domain affected microtubule binding, whereas a monoclonal mouse antibody specific for the N-terminal domain did not. Together with steric considerations, this suggests that the microtubule-interacting doublecortin domain observed in cryo-electron micrographs is the C-terminal domain rather than the N-terminal one.

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Organizational Affiliation: 

From the pRED Pharma Research and Early Development, Therapeutic Modalities, and [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuronal migration protein doublecortin	A, B	105	Homo sapiens	Mutation(s): 2  Gene Names: DCX, DBCN, LISX
UniProt & NIH Common Fund Data Resources
Find proteins for O43602 (Homo sapiens) Explore O43602  Go to UniProtKB:  O43602
PHAROS:  O43602 GTEx:  ENSG00000077279

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.236 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.156	α = 90
b = 82.156	β = 90
c = 139.897	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SADABS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-03-07 
• Released Date: 2016-03-23 
Deposition Author(s): Ruf, A., Benz, J., Burger, D., D'Arcy, B., Debulpaep, M., Di Lello, P., Fry, D., Huber, W., Kremer, T., Laeremans, T., Matile, H., Ross, A., Rudolph, M.G., Rufer, A.C., Sharma, A., Steinmetz, M.O., Steyaert, J., Schoch, G., Stihle, M., Thoma, R.

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Funding Organization	Location	Grant Number
European Molecular Biology Organization	Switzerland	LongTerm Fellowship
Swiss National Science Foundation	Switzerland	310030B_138659

Revision History  

• Version 1.0: 2016-03-23
  Type: Initial release
  
• Version 1.1: 2016-05-18
  Changes: Database references
• Version 1.2: 2016-06-08
  Changes: Database references
• Version 1.3: 2016-08-10
  Changes: Database references
• Version 1.4: 2016-12-14
  Changes: Structure summary
• Version 1.5: 2017-09-06
  Changes: Author supporting evidence